Refactor code to improve compatibility and maintainability:

- Update CI configuration to support Python 3.8-3.12 and actions versions.
- Replace deprecated `imp` module with modern imports in analyzeSBML.py and libsbml2bngl.py.
- Introduce utility functions `get_size` and `get_item` for better handling of object sizes and indexing.
- Update SBML2BNGL class to utilize new utility functions for size retrieval.
- Enhance error handling in tests to provide clearer output on exceptions.

Author: akutuva21

.github/workflows/ci.yml

@@ -21,17 +21,17 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache pip
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('requirements-dev.txt') }}

bionetgen/atomizer/atomizer/analyzeSBML.py

@@ -6,7 +6,6 @@
 """
 
 import enum
-import imp
 from pyparsing import Word, Suppress, Optional, alphanums, Group, ZeroOrMore
 import numpy as np
 import json

bionetgen/atomizer/libsbml2bngl.py

@@ -7,7 +7,6 @@
 
 #!/usr/bin/env python
 from collections import OrderedDict
-from telnetlib import IP
 import time
 import libsbml
 import bionetgen.atomizer.writer.bnglWriter as writer

bionetgen/atomizer/sbml2bngl.py

@@ -12,7 +12,7 @@
 from collections import Counter
 from collections import defaultdict
 import math as pymath
-from bionetgen.atomizer.utils.util import logMess, TranslationException
+from bionetgen.atomizer.utils.util import logMess, TranslationException, get_size, get_item
 import libsbml
 from bionetgen.atomizer.bngModel import bngModel
 
@@ -220,7 +220,7 @@ def extractModelAnnotation(self):
         annotation = self.model.getAnnotation()
         lista = libsbml.CVTermList()
         libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
-        for idx in range(lista.getSize()):
+        for idx in range(get_size(lista)):
             # biol,qual = lista.get(idx).getBiologicalQualifierType(), lista.get(idx).getModelQualifierType()
             qualifierType = lista.get(idx).getQualifierType()
             qualifierDescription = (
@@ -230,8 +230,8 @@ def extractModelAnnotation(self):
             )
             if qualifierDescription not in metaInformation:
                 metaInformation[qualifierDescription] = set([])
-            for idx2 in range(0, lista.get(idx).getResources().getLength()):
-                resource = lista.get(idx).getResources().getValue(idx2)
+            for idx2 in range(0, get_size(get_item(lista, idx).getResources())):
+                resource = get_item(lista, idx).getResources().getValue(idx2)
                 metaInformation[qualifierDescription].add(resource)
         return metaInformation
 
@@ -338,7 +338,7 @@ def getRawSpecies(self, species, parameters=[], logEntries=True):
         # by compartment
         if logEntries and standardizedName != "0":
             if standardizedName in self.speciesMemory:
-                if len(list(self.model.getListOfCompartments())) == 1:
+                if get_size(self.model.getListOfCompartments()) == 1:
                     standardizedName += "_" + species.getId()
                 else:
                     # we can differentiate by compartment tag, no need to attach it to the name
@@ -649,23 +649,9 @@ def find_all_symbols(self, math, reactionID):
             )
         l = math.getListOfNodes()
         replace_dict = {}
-
-        # libSBML versions differ in how list-like objects expose size/length
-        if hasattr(l, "getSize"):
-            size = l.getSize()
-        elif hasattr(l, "size"):
-            size = l.size()
-        else:
-            try:
-                size = len(l)
-            except Exception:
-                size = 0
-
+        size = get_size(l)
         for inode in range(size):
-            if hasattr(l, "get"):
-                node = l.get(inode)
-            else:
-                node = l[inode]
+            node = get_item(l, inode)
             # Sympy doesn't like "def" in our string
             name = node.getName()
             if name == "def":
@@ -1293,9 +1279,9 @@ def __getRawRules(
                 for compartment in (self.model.getListOfCompartments()):
                     if compartment.getId() not in compartmentList:
                         if len(rReactant) != 2:
-                            rateL = '{0} * {1}'.format(rateL,compartment.getSize())
+                            rateL = '{0} * {1}'.format(rateL, get_size(compartment))
                         if len(rProduct) != 2:
-                             rateR = '{0} * {1}'.format(rateR,compartment.getSize())
+                             rateR = '{0} * {1}'.format(rateR,get_size(compartment))
             """
         return {
             "reactants": reactant,
@@ -1621,7 +1607,7 @@ def __getRawCompartments(self, compartment):
         """
         idid = compartment.getId()
         name = compartment.getName()
-        size = compartment.getSize()
+        size = get_size(compartment)
         # volume messes up the reactions
         # size = 1.0
         dimensions = compartment.getSpatialDimensions()
@@ -2871,7 +2857,7 @@ def check_noCompartment(self, parameters=[]):
             self.bngModel.noCompartment = True
             return
         for compartment in self.model.getListOfCompartments():
-            self.compartmentDict[compartment.getId()] = compartment.getSize()
+            self.compartmentDict[compartment.getId()] = get_size(compartment)
         self.noCompartment = False
         self.bngModel.noCompartment = False
         # Get all rawSpecies
@@ -2945,7 +2931,7 @@ def default_to_regular(d):
         speciesAnnotationInfo = default_to_regular(self.getFullAnnotation())
         annotationInfo = {"moleculeTypes": {}, "species": {}}
         for compartment in self.model.getListOfCompartments():
-            compartmentDict[compartment.getId()] = compartment.getSize()
+            compartmentDict[compartment.getId()] = get_size(compartment)
         unitFlag = True
         for species in self.model.getListOfSpecies():
             # making molecule and seed species objs for
@@ -2971,7 +2957,7 @@ def default_to_regular(d):
                 if rawSpecies["returnID"] in rawSpeciesName:
                     rawSpeciesName.remove(rawSpecies["returnID"])
                 if (
-                    translator[rawSpecies["returnID"]].getSize() == 1
+                    get_size(translator[rawSpecies["returnID"]]) == 1
                     and translator[rawSpecies["returnID"]].molecules[0].name
                     not in names
                     and translator[rawSpecies["returnID"]].molecules[0].name
@@ -3086,9 +3072,9 @@ def default_to_regular(d):
                         if self.noCompartment:
                             compartmentSize = 1.0
                         else:
-                            compartmentSize = self.model.getCompartment(
-                                rawSpecies["compartment"]
-                            ).getSize()
+                            compartmentSize = get_size(
+                                self.model.getCompartment(rawSpecies["compartment"])
+                            )
                         newParameter = compartmentSize * newParameter
                         # temp testing AS
                         spec_obj.val = newParameter
@@ -3261,7 +3247,7 @@ def default_to_regular(d):
         sorted(rawSpeciesName, key=len)
         for species in rawSpeciesName:
             if (
-                translator[species].getSize() == 1
+                get_size(translator[species]) == 1
                 and translator[species].molecules[0].name not in names
             ):
                 names.append(translator[species].molecules[0].name)
@@ -3401,10 +3387,10 @@ def getSpeciesAnnotation(self):
             annotationXML = species.getAnnotation()
             lista = libsbml.CVTermList()
             libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
-            if lista.getSize() == 0:
+            if get_size(lista) == 0:
                 self.speciesAnnotation[rawSpecies["returnID"]] = []
             else:
-                for idx in range(lista.getSize()):
+                for idx in range(get_size(lista)):
                     self.speciesAnnotation[rawSpecies["returnID"]].append(
                         lista.get(idx).getResources()
                     )
@@ -3421,11 +3407,11 @@ def getFullAnnotation(self):
             annotationXML = species.getAnnotation()
             lista = libsbml.CVTermList()
             libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
-            if lista.getSize() == 0:
+            if get_size(lista) == 0:
                 continue
             else:
-                for idx in range(lista.getSize()):
-                    for idx2 in range(0, lista.get(idx).getResources().getLength()):
+                for idx in range(get_size(lista)):
+                    for idx2 in range(0, get_size(get_item(lista, idx).getResources())):
                         resource = lista.get(idx).getResources().getValue(idx2)
                         qualifierType = lista.get(idx).getQualifierType()
                         qualifierDescription = (
@@ -3444,7 +3430,7 @@ def getModelAnnotation(self):
         annotationXML = self.model.getAnnotation()
         lista = libsbml.CVTermList()
         libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
-        if lista.getSize() == 0:
+        if get_size(lista) == 0:
             modelAnnotations = []
         else:
             tempDict = {}

bionetgen/atomizer/sbml2json.py

@@ -8,6 +8,7 @@
 import libsbml
 import json
 from optparse import OptionParser
+from .utils.util import get_size
 
 
 def factorial(x):
@@ -114,7 +115,7 @@ def __getRawCompartments(self):
         compartmentList = {}
         for compartment in self.model.getListOfCompartments():
             name = compartment.getId()
-            size = compartment.getSize()
+            size = get_size(compartment)
             outside = compartment.getOutside()
             dimensions = compartment.getSpatialDimensions()
             compartmentList[name] = [dimensions, size, outside]

bionetgen/atomizer/utils/annotationDeletion.py

@@ -8,7 +8,7 @@
 import progressbar
 
 import libsbml
-from util import logMess
+from util import logMess, get_size, get_item
 from sbml2bngl import SBML2BNGL as SBML2BNGL
 import structures
 import atomizer.moleculeCreation as mc
@@ -125,15 +125,15 @@ def parseAnnotation(annotation):
     speciesAnnotationDict = defaultdict(list)
     lista = libsbml.CVTermList()
     libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
-    for idx in range(0, lista.getSize()):
-        for idx2 in range(0, lista.get(idx).getResources().getLength()):
-            resource = lista.get(idx).getResources().getValue(idx2)
+    for idx in range(0, get_size(lista)):
+        for idx2 in range(0, get_size(get_item(lista, idx).getResources())):
+            resource = get_item(lista, idx).getResources().getValue(idx2)
 
-            qualifierType = lista.get(idx).getQualifierType()
+            qualifierType = get_item(lista, idx).getQualifierType()
             qualifierDescription = (
-                bioqual[lista.get(idx).getBiologicalQualifierType()]
+                bioqual[get_item(lista, idx).getBiologicalQualifierType()]
                 if qualifierType
-                else modqual[lista.get(idx).getModelQualifierType()]
+                else modqual[get_item(lista, idx).getModelQualifierType()]
             )
             speciesAnnotationDict[qualifierDescription].append(resource)
     return speciesAnnotationDict

bionetgen/atomizer/utils/annotationExtender.py

@@ -6,7 +6,7 @@
 """
 
 import libsbml
-from util import logMess
+from util import logMess, get_size, get_item
 from sbml2bngl import SBML2BNGL as SBML2BNGL
 import structures
 import atomizer.resolveSCT as mc
@@ -128,15 +128,15 @@ def parseAnnotation(annotation):
     speciesAnnotationDict = defaultdict(list)
     lista = libsbml.CVTermList()
     libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
-    for idx in range(0, lista.getSize()):
-        for idx2 in range(0, lista.get(idx).getResources().getLength()):
-            resource = lista.get(idx).getResources().getValue(idx2)
+    for idx in range(0, get_size(lista)):
+        for idx2 in range(0, get_size(get_item(lista, idx).getResources())):
+            resource = get_item(lista, idx).getResources().getValue(idx2)
 
-            qualifierType = lista.get(idx).getQualifierType()
+            qualifierType = get_item(lista, idx).getQualifierType()
             qualifierDescription = (
-                bioqual[lista.get(idx).getBiologicalQualifierType()]
+                bioqual[get_item(lista, idx).getBiologicalQualifierType()]
                 if qualifierType
-                else modqual[lista.get(idx).getModelQualifierType()]
+                else modqual[get_item(lista, idx).getModelQualifierType()]
             )
             speciesAnnotationDict[qualifierDescription].append(resource)
     return speciesAnnotationDict

bionetgen/atomizer/utils/annotationExtractor.py

@@ -7,6 +7,7 @@
 
 import libsbml
 from sbml2bngl import SBML2BNGL as SBML2BNGL
+from .util import get_size, get_item
 import structures
 import atomizer.moleculeCreation as mc
 import os
@@ -96,14 +97,14 @@ def parseAnnotation(self, annotation):
         lista = libsbml.CVTermList()
         libsbml.RDFAnnotationParser.parseRDFAnnotation(annotation, lista)
         # print '----',species.getName()
-        for idx in range(0, lista.getSize()):
-            for idx2 in range(0, lista.get(idx).getResources().getLength()):
-                resource = lista.get(idx).getResources().getValue(idx2)
-                qualifierType = lista.get(idx).getQualifierType()
+        for idx in range(0, get_size(lista)):
+            for idx2 in range(0, get_size(get_item(lista, idx).getResources())):
+                resource = get_item(lista, idx).getResources().getValue(idx2)
+                qualifierType = get_item(lista, idx).getQualifierType()
                 qualifierDescription = (
-                    bioqual[lista.get(idx).getBiologicalQualifierType()]
+                    bioqual[get_item(lista, idx).getBiologicalQualifierType()]
                     if qualifierType
-                    else modqual[lista.get(idx).getModelQualifierType()]
+                    else modqual[get_item(lista, idx).getModelQualifierType()]
                 )
                 speciesAnnotationDict[qualifierDescription].append(resource)
         return speciesAnnotationDict
@@ -294,20 +295,20 @@ def getModelAnnotations(self):
         lista = libsbml.CVTermList()
         libsbml.RDFAnnotationParser.parseRDFAnnotation(annotationXML, lista)
         modelAnnotations = []
-        for idx in range(lista.getSize()):
-            for idx2 in range(lista.get(idx).getResources().getLength()):
-                if lista.get(idx).getQualifierType():
+        for idx in range(get_size(lista)):
+            for idx2 in range(get_size(get_item(lista, idx).getResources())):
+                if get_item(lista, idx).getQualifierType():
                     modelAnnotations.append(
                         [
-                            bioqual[lista.get(idx).getBiologicalQualifierType()],
-                            lista.get(idx).getResources().getValue(idx2),
+                            bioqual[get_item(lista, idx).getBiologicalQualifierType()],
+                            get_item(lista, idx).getResources().getValue(idx2),
                         ]
                     )
                 else:
                     modelAnnotations.append(
                         [
-                            modqual[lista.get(idx).getModelQualifierType()],
-                            lista.get(idx).getResources().getValue(idx2),
+                            modqual[get_item(lista, idx).getModelQualifierType()],
+                            get_item(lista, idx).getResources().getValue(idx2),
                         ]
                     )
 

bionetgen/atomizer/utils/util.py

@@ -321,6 +321,27 @@ def logMess(logType, logMessage):
         logger.error(logMessage, loc=f"{__file__} : {module}.logMess()")
 
 
+def get_size(obj):
+    if hasattr(obj, "getSize"):
+        return obj.getSize()
+    elif hasattr(obj, "size"):
+        return obj.size()
+    elif hasattr(obj, "getLength"):
+        return obj.getLength()
+    else:
+        try:
+            return len(obj)
+        except:
+            return 0
+
+
+def get_item(obj, idx):
+    if hasattr(obj, "get"):
+        return obj.get(idx)
+    else:
+        return obj[idx]
+
+
 def testBNGFailure(fileName):
     with open(os.devnull, "w") as f:
         result = call(["bngdev", fileName], stdout=f)